However, these findings do not contradict the fact that Chimps are our close cousins, these findings just confirm that the Y evolves much faster than the rest of the genome. Wiki puts it this way:

The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater risk of mutation than the rest of the genome.[12] The increased mutation risk for the Y chromosome is reported by Graves as a factor 4.8.[12] However, her original reference obtains this number for the relative mutation rates in male and female germ lines for the lineage leading to humans.[20]